Vulnerable marine ecosystems (VMEs) are protected from bottom-fishing impacts in international waters by UN resolutions through Regional Fishery Management Organizations. VMEs include deep-sea benthic taxa whose life-history traits make them vulnerable to disturbance. Conservation measures for VMEs require regulatory frameworks informed by biodiversity maps. Here we evaluate biogeographic patterns of deep-sea benthic biodiversity of the Southern Indian Ocean to understand conservation avenues for the Southern Indian Ocean Fisheries Agreement (SIOFA) management organization. We synthesised knowledge on the distribution of benthic deep-sea taxa and explored the quality and quantity of available data. Next, we explored how taxa are structured into bioregions using biogeographical networks. We found astounding Wallacean and Linnaean shortfalls within SIOFA’s management area, which is virtually devoid of distributional data. Across the entire area, results suggest that only 73% of the expected deep-sea taxa has been sampled, and most sampled cells appeared to be inadequately sampled. Yet, our bioregionalization analysis identified multiple bioregions, some only observed within SIOFA’s area. The Wallacean and Linnean shortfalls are so important for VMEs that they severely impede to make adequate maps for conservation planning. Bioregionalization results suggest that SIOFA hosts a unique faunal composition that must be safeguarded. Predictive approaches to compensate for these shortfalls exist but will likely be insufficient and uncertain. Within SIOFA’s area, there is no satisfying solution to cope with the data shortfalls. Yet, biodiversity maps are a global responsibility. This study makes a call to invest in biodiversity inventories in this world’s region to promote informed policy-making decisions.